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Ping Q, Zhang Z, Guo W, Wang L, Li Y. A comprehensive investigation to the fate of phosphorus in full-scale wastewater treatment plants using aluminum salts for enhanced phosphorus removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169641. [PMID: 38159765 DOI: 10.1016/j.scitotenv.2023.169641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
This study investigated the fate of phosphorus (P) in 8 full-scale municipal wastewater treatment plants (WWTPs) in Shanghai, China, in which both biological nutrient removal and aluminum-based chemical phosphorus removal were used. The results showed that 83.8-98.9 % P was transferred to the sludge in the 8 WWTPs by both chemical and biological reactions. P speciation analysis indicated that chemical P precipitates accounted for 84.3 % in the activated sludge, of which crystalline AlPO4 and amorphous iron‑phosphorus compounds (FePs) were the main components. Sludge with more water-soluble and weakly adsorbed P was generated in the anaerobic-anoxic-oxic (A/A/O) process than in other processes. Among the 8 WWTPs, the one with the largest flow rate and relatively short sludge retention time (SRT) had the best potential to release P from all types of sludge. The recovery potential of P from thickened sludge can be improved by separately thickening the sludge produced in the high-efficiency sedimentation tank or feeding it into the dewatering process directly. Different P removal chemicals and dosing points changed the amount of chemical precipitate formed but had little effect on the composition of P accumulating organisms (PAOs) at the genus level. Although aluminum-based coagulants were applied in the investigated WWTPs, Fe in wastewater had the most positive effect on the proliferation of PAOs. The synthesis of polyphosphate was also related to the metabolism of PAOs as it affected transmembrane inorganic phosphate (Pi) transport and polyhydroxybutyrate (PHB) synthesis. The in-depth understanding of the fate of P is beneficial to improve P recovery efficiency in WWTPs.
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Affiliation(s)
- Qian Ping
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Zhipeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environment in Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, PR China
| | - Wenjie Guo
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Lin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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Xie X, Deng X, Chen J, Chen L, Yuan J, Chen H, Wei C, Liu X, Qiu G. Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into Candidatus Accumulibacter. ISME COMMUNICATIONS 2024; 4:ycae049. [PMID: 38808122 PMCID: PMC11131965 DOI: 10.1093/ismeco/ycae049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024]
Abstract
Candidatus Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality Ca. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the Ca. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that Ca. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying Ca. Accumulibacter. A pan-genomic analysis with other Ca. Accumulibacter members suggested that all Ca. Accumulibacter likely has the potential to use dicarboxylic amino acids. Ca. Accumulibacter aalborgensis AALB and Ca. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for Ca. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of Ca. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.
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Affiliation(s)
- Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jinling Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
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Zhang X, Li X, Zhang L, Peng Y. Enhancing nitrogen removal performance through intermittent aeration in continuous plug-flow anaerobic/aerobic/anoxic process treating low-strength municipal sewage. BIORESOURCE TECHNOLOGY 2024; 391:129979. [PMID: 37926355 DOI: 10.1016/j.biortech.2023.129979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
Advanced nitrogen removal cannot be achieved through the conventional biological nitrogen removal process, which requires higher carbon sources and aeration energy. The proposal of intermittent aeration in the aerobic chambers offered an innovative approach to enhance nitrogen removal in low carbon-to-nitrogen ratio (C/N) municipal sewage, using a plug-flow reactor with anaerobic/aerobic/anoxic (AOA) process. Due to the effective utilization of internal carbon sources through the intermittent aeration, the total inorganic nitrogen removal efficiency (NRE) increased to 77.9 ± 3.2 % with the mean aerobic hydraulic retention time of only 3.2 h and a low C/N of 3.3 during the operation of 210 days. Polyhydroxyalkanoates dominated the nitrogen removal in this AOA system, accounting for 48.0 %, primarily occurring in the alternant aerobic/anoxic chambers. Moreover, the microbial community structure remained unchanged while the NRE increased to 77.9 %. This study provided an efficient and economic strategy for the continuous plug-flow AOA process.
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Affiliation(s)
- Xiyue Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Xiyao Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Liang Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China.
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4
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Chen L, Wei G, Zhang Y, Wang K, Wang C, Deng X, Li Y, Xie X, Chen J, Huang F, Chen H, Zhang B, Wei C, Qiu G. Candidatus Accumulibacter use fermentation products for enhanced biological phosphorus removal. WATER RESEARCH 2023; 246:120713. [PMID: 37839225 DOI: 10.1016/j.watres.2023.120713] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/17/2023] [Accepted: 10/07/2023] [Indexed: 10/17/2023]
Abstract
Previous research suggested that two major groups of polyphosphate-accumulating organisms (PAOs), i.e., Ca. Accumulibacter and Tetrasphaera, play cooperative roles in enhanced biological phosphorus removal (EBPR). The fermentation of complex organic compounds by Tetrasphaera provides carbon sources for Ca. Accumulibacter. However, the viability of the fermentation products (e.g., lactate, succinate, alanine) as carbon sources for Ca. Accumulibacter and their potential effects on the metabolism of Ca. Accumulibacter were largely unknown. This work for the first time investigated the capability and metabolic details of Ca. Accumulibacter cognatus clade IIC strain SCUT-2 (enriched in a lab-scale reactor with a relative abundance of 42.8%) in using these fermentation products for EBPR. The enrichment culture was able to assimilate lactate and succinate with the anaerobic P release to carbon uptake ratios of 0.28 and 0.36 P mol/C mol, respectively. In the co-presence of acetate, the uptake of lactate was strongly inhibited, since two substrates shared the same transporter as suggested by the carbon uptake bioenergetic analysis. When acetate and succinate were fed at the same time, Ca. Accumulibacter assimilated two carbon sources simultaneously. Proton motive force (PMF) was the key driving force (up to 90%) for the uptake of lactate and succinate by Ca. Accumulibacter. Apart from the efflux of proton in symport with phosphate via the inorganic phosphate transport system, translocation of proton via the activity of fumarate reductase contributed to the generation of PMF, which agreed with the fact that PHV was a major component of PHA when lactate and succinate were used as carbon sources, involving the succinate-propionate pathway. Metabolic models for the usage of lactate and succinate by Ca. Accumulibacter for EBPR were built based on the combined physiological, biochemical, metagenomic, and metatranscriptomic analyses. Alanine was shown as an invalid carbon source for Ca. Accumulibacter. Instead, it significantly and adversely affected Ca. Accumulibacter-mediated EBPR. Phosphate release was observed without alanine uptake. Significant inhibitions on the aerobic phosphate uptake was also evident. Overall, this study suggested that there might not be a simply synergic relationship between Ca. Accumulibacter and Tetrasphaera. Their interactions would largely be determined by the kind of fermentation products released by the latter.
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Affiliation(s)
- Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Gengrui Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Yushen Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Kaiying Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Cenchao Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Yaqian Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Jinling Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Fu Huang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Bin Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, PR China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, PR China.
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, PR China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, PR China.
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5
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Sharma P, Vishwakarma R, Varjani S, Gautam K, Gaur VK, Farooqui A, Sindhu R, Binod P, Awasthi MK, Chaturvedi P, Pandey A. Multi-omics approaches for remediation of bisphenol A: Toxicity, risk analysis, road blocks and research perspectives. ENVIRONMENTAL RESEARCH 2022; 215:114198. [PMID: 36063912 DOI: 10.1016/j.envres.2022.114198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/01/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
In this "plastic era" with the increased use of plastic in day today's life the accumulation of its degraded products like microplastics or plastic additives such as Bisphenol A(BPA) is also increasing. BPA is an endocrine-disrupting chemical used as a plasticizing agent in clear plastic, building materials, coatings, and epoxy resin. Several enzymes including laccases and lipases have been studied for the reduction of BPA toxicity. Over the decades of encountering these toxicants, microorganisms have evolved to degrade different classes of plastic additives. Since the degradation of BPA is a long process thus meta-omics approaches have been employed to identify the active microbiota and microbial dynamics involved in the mitigation of BPA. It is also necessary to investigate the impact of processing activities on transit of BPA in food items and to limit its entrance in food world. This review summarizes a comprehensive overview on BPA sources, toxicity, bio-based mitigation approaches along with a deeper understanding of multi-omics approaches for its reduction and risk analysis. Knowledge gaps and opportunities have been comprehensively compiled that would aid the state-of-the-art information in the available literature for the researchers to further address this issue.
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Affiliation(s)
- Poonam Sharma
- Department of Bioengineering, Integral University, Lucknow, 226 026, India
| | - Reena Vishwakarma
- Department of Bioengineering, Integral University, Lucknow, 226 026, India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, 382 010, India.
| | - Krishna Gautam
- Centre of Energy and Environmental Sustainability, Lucknow, 226 021, India
| | - Vivek K Gaur
- Centre of Energy and Environmental Sustainability, Lucknow, 226 021, India; School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Alvina Farooqui
- Department of Bioengineering, Integral University, Lucknow, 226 026, India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam, 691 505, Kerala, India
| | - Parameswaran Binod
- CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, 695 019, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A& F University, Yangling, Shaanxi Province, 712100, PR China
| | - Preeti Chaturvedi
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Ashok Pandey
- Centre of Energy and Environmental Sustainability, Lucknow, 226 021, India; Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, India
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6
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Dong X, Huang Z, Peng X, Jia X. Advanced simultaneous nitrogen and phosphorus removal for non-sterile wastewater through a novel coupled yeast-sludge system: Performance, microbial interaction, and mechanism. CHEMOSPHERE 2022; 309:136645. [PMID: 36183892 DOI: 10.1016/j.chemosphere.2022.136645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 09/17/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
A novel coupled yeast-sludge system (CYSS) was constructed by the yeast Candida sp. PNY integrated with activated sludge to treat non-sterile mainstream wastewater. After 240-day cultivation, compared with single activated sludge, simultaneous removal efficiency of total organic carbon (TOC), nitrogen and phosphorus increased by 19.5% (176.34 mg TOC g-1 d-1), 21.3% (11.25 mg TN g-1 d-1) and 15.0% (6.95 mg TP g-1 d-1), respectively, while the amount of sludge reduced by 50%. Amplicon sequencing analysis showed that the abundance of Nitrosomonas, Nitrospira, Zoogloea, Dechloromonas, and Candidatus Accumulibacter significantly decreased to 0% on Day 200. Abundance of nirS and nirK for denitrification significantly decreased in CYSS by quantitative PCR (qPCR), and the copies of nirS and nirK were 3.37-fold and 1.71-fold decrease from Day 0 to Day 240, respectively. The results of Fluorescence in situ hybridization and co-occurrence network showed that Candida sp. PNY predominated its distribution in CYSS, and strongly connected with environmental variables based on network analysis. Furthermore, this study reconstructed the carbon, nitrogen and phosphorus metabolic pathways of the CYSS based on metagenomics.
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Affiliation(s)
- Xiaoqi Dong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zidan Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Xiaoshan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China
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7
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Yang Y, Liu J, Xue T, Hanamoto S, Wang H, Sun P, Zhao L. Complex behavior between microplastic and antibiotic and their effect on phosphorus-removing Shewanella strain during wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157260. [PMID: 35820524 DOI: 10.1016/j.scitotenv.2022.157260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Owing to their widespread application and use, microplastics (MPs) and antibiotics coexist in the sewage treatment systems. In this study, the effects and mechanisms of the combined stress of MPs and ciprofloxacin (CIP) on phosphorus removal by phosphorus-accumulating organisms (PAOs) were investigated. This study found that the four types of MPs and CIP exhibited different antagonistic effects on the inhibition of phosphorus removal by PAO. MPs reduced the effective concentration of CIP through adsorption and thus reduced its toxicity, which was affected by the biofilms on MPs. In addition, CIP may cause PAO to produce more extracellular polymeric substances, which reduces the physical and oxidative stress of MPs on PAO. Our results are helpful as they increase the understanding of the effects of complex emerging pollutants in sewage systems and propose measures to strengthen the biological phosphorus removal in sewage treatment processes.
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Affiliation(s)
- Yongkui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
| | - Jinyi Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Tongyu Xue
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Seiya Hanamoto
- Environment Preservation Center, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Hongyang Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Peizhe Sun
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Lin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
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Dai C, Wu H, Wang X, Zhao K, Lu Z. Network and meta-omics reveal the cooperation patterns and mechanisms in an efficient 1,4-dioxane-degrading microbial consortium. CHEMOSPHERE 2022; 301:134723. [PMID: 35489450 DOI: 10.1016/j.chemosphere.2022.134723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/09/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
1,4-Dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mixed cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial consortium CH1. A 1,4-dioxane-degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and had a potential of being one of the important degraders due to its high relative abundance, highly expressed monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium could be involved in the intermediates metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) differentially high-expressed. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators cooperated with ZM13 in the way of providing amino acids or fatty acids, as well as relieving environmental stresses to promote biodegradation. These results provide new insights into our understandings of the microbial interactions during 1,4-dioxane degradation, and have important implications for predicting microbial cooperation and constructing efficient and stable synthetic 1,4-dioxane-degrading consortia for practical remediation.
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Affiliation(s)
- Chuhan Dai
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China.
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Ni M, Chen Y, Pan Y, Huang Y, Li DP, Li L, Huang B, Song Z. Study on community structure and metabolic mechanism of dominant polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in suspended biofilm based on phosphate recovery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152678. [PMID: 34973331 DOI: 10.1016/j.scitotenv.2021.152678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 05/16/2023]
Abstract
Biofilm sequencing batch reactor (BSBR) can achieve efficient phosphate (P) removal and enrichment, but its process performance and metabolic mechanisms for P removal and enrichment of municipal wastewater remain largely unclear. In the present study, we assessed the P removal and enrichment of municipal wastewater at influent P concentrations of 2.5 mg/L and 10 mg/L. The efficiency of P removal and enzyme activity in polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) were compared, and the growth and metabolic characteristics of dominant PAOs and GAOs at different influent P concentrations were studied with the macro-sequencing technology. The results showed that the P recovery efficiencies were 70.03% and 76.19% when the influent P concentration was 2.5 mg/L and 10 mg/L in BSBR, respectively, and the maximum P concentration of recovery liquid was 81.29 mg/L and 173.12 mg/L, respectively. There were no phosphate kinase (PPK) and phosphate hydrolase (PPX) in extracellular polymeric substances (EPS). The dominant PAOs were Candidatus_Contendobacter, Dechloromonas, and Flavobacterium, and the dominant GAO was Candidatus_Competibacter. The abundance of Candidatus_Contendobacter was the highest with the most potential contribution to P removal. PAOs had competitive advantages in carbon (C) source uptake, glycogen metabolism, P metabolism, and adenosine triphosphate (ATP) metabolism. HMP was unique to PAOs, EMP had the highest abundance in glycogen metabolism, and ED was contained in PAOs of BSBR. These results indicated that BSBR provided sufficient reducing power and ATP for PAOs through different glycogen decomposition pathways to promote P uptake and obtained competitive advantages in P metabolism, C source uptake, and ATP utilization to achieve efficient P removal and enrichment. Collectively, our current findings provided valuable insights into the P removal and enrichment mechanism of BSBR in municipal sewage.
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Affiliation(s)
- Min Ni
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; Jiangsu Key Laboratory of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Yue Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Yang Pan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, China.
| | - Yong Huang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, China
| | - Da-Peng Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, China
| | - Lu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Bo Huang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
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10
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He Y, Song Z, Dong X, Zheng Q, Peng X, Jia X. Candida tropicalis prompted effectively simultaneous removal of carbon, nitrogen and phosphorus in activated sludge reactor: Microbial community succession and functional characteristics. BIORESOURCE TECHNOLOGY 2022; 348:126820. [PMID: 35134527 DOI: 10.1016/j.biortech.2022.126820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
A new Candida tropicalis that simultaneously remove nitrogen and phosphorus, and degrade organic matters was isolated. Three continuous stirred tank reactors inoculated with C. tropicalis, activated sludge, and their co-existing system in aerobic condition were operated for 150 days. Results demonstrated that the inoculation of C. tropicalis in the co-existing system remarkably improved the carbon, nitrogen, and phosphorus removal efficiencies. The co-existing system had increased carbon, nitrogen, and phosphorus removal efficiencies (92%, 73%, and 63%, respectively); decreased biomass (reduced from 1200 mg/L to 500 mg/L); and C. tropicalis as the dominant strain. The relative abundance of traditional nitrogen- and phosphorus-removing microorganisms, such as Mycobacterium, Flavonifactor, and Devsia, increased in the co-existing system. Metagenomic analysis showed that the presence of the PCYT2, EPT1, and phnPP genes and more complexed metabolism pathways in the co-existing system might be responsible for the more activated metabolism process.
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Affiliation(s)
- Yuzhe He
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhaohong Song
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoqi Dong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Qihang Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
| | - Xiaoshan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
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11
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Ni M, Pan Y, Chen Y, Zhang X, Huang Y, Song Z. Effects of seasonal temperature variations on phosphorus removal, recovery, and key metabolic pathways in the suspended biofilm. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Song Y, Jiang CY, Liang ZL, Zhu HZ, Jiang Y, Yin Y, Qin YL, Huang HJ, Wang BJ, Wei ZY, Cheng RX, Liu ZP, Liu Y, Jin T, Wang AJ, Liu SJ. Candidatus Kaistella beijingensis sp. nov., Isolated from a Municipal Wastewater Treatment Plant, Is Involved in Sludge Foaming. Appl Environ Microbiol 2021; 87:e0153421. [PMID: 34586909 PMCID: PMC8612268 DOI: 10.1128/aem.01534-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 12/30/2022] Open
Abstract
Biological foaming (or biofoaming) is a frequently occurring problem in wastewater treatment plants (WWTPs) and is attributed to the overwhelming growth of filamentous bulking and foaming bacteria (BFB). Biological foaming has been intensively investigated, with BFB like Microthrix and Skermania having been identified from WWTPs and implicated in foaming. Nevertheless, studies are still needed to improve our understanding of the microbial diversity of WWTP biofoams and how microbial activities contribute to foaming. In this study, sludge foaming at the Qinghe WWTP of China was monitored, and sludge foams were investigated using culture-dependent and culture-independent microbiological methods. The foam microbiomes exhibited high abundances of Skermania, Mycobacterium, Flavobacteriales, and Kaistella. A previously unknown bacterium, Candidatus Kaistella beijingensis, was cultivated from foams, its genome was sequenced, and it was phenotypically characterized. Ca. K. beijingensis exhibits hydrophobic cell surfaces, produces extracellular polymeric substances (EPS), and metabolizes lipids. Ca. K. beijingensis abundances were proportional to EPS levels in foams. Several proteins encoded by the Ca. K. beijingensis genome were identified from EPS that was extracted from sludge foams. Ca. K. beijingensis populations accounted for 4 to 6% of the total bacterial populations in sludge foam samples within the Qinghe WWTP, although their abundances were higher in spring than in other seasons. Cooccurrence analysis indicated that Ca. K. beijingensis was not a core node among the WWTP community network, but its abundances were negatively correlated with those of the well-studied BFB Skermania piniformis among cross-season Qinghe WWTP communities. IMPORTANCE Biological foaming, also known as scumming, is a sludge separation problem that has become the subject of major concern for long-term stable activated sludge operation in decades. Biological foaming was considered induced by foaming bacteria. However, the occurrence and deterioration of foaming in many WWTPs are still not completely understood. Cultivation and characterization of the enriched bacteria in foaming are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the understanding of their relationships with foaming and performance of WWTPs.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- The Ecology and Environment Branch of State Center for Research and Development of Oil Shale Exploitation, PetroChina Planning and Engineering Institute, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, China
| | - Ye Yin
- BGI-Qingdao, Qingdao, China
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zi-Yan Wei
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rui-Xue Cheng
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, China
| | | | - Ai-Jie Wang
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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13
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Srinivasan VN, Li G, Wang D, Tooker NB, Dai Z, Onnis-Hayden A, Bott C, Dombrowski P, Schauer P, Pinto A, Gu AZ. Oligotyping and metagenomics reveal distinct Candidatus Accumulibacter communities in side-stream versus conventional full-scale enhanced biological phosphorus removal (EBPR) systems. WATER RESEARCH 2021; 206:117725. [PMID: 34653799 DOI: 10.1016/j.watres.2021.117725] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Candidatus Accumulibacter phosphatis (CAP) and its clade-level micro-diversity has been associated with and implicated in functional differences in phosphorus removal performance in enhanced biological phosphorus removal (EBPR) systems. Side-stream EBPR (S2EBPR) is an emerging process that has been shown to present a suite of advantages over the conventional EBPR design, however, large knowledge gaps remain in terms of its underlying ecological mechanisms. Here, we compared and revealed the higher-resolution differences in microbial ecology of CAP between a full-scale side-stream EBPR configuration and a conventional A2O EBPR process that were operated in parallel and with the same influent feed. Even though the relative abundance of CAP, revealed by 16S rRNA gene amplicon sequencing, was similar in both treatment trains, a clade-level analysis, using combined 16S rRNA-gene based amplicon sequencing and oligotyping analysis and metagenomics analysis, revealed the distinct CAP microdiversity between the S2EBPR and A2O configurations that likely attributed to the improved performance in S2EBPR in comparison to conventional EBPR. Furthermore, genome-resolved metagenomics enabled extraction of three metagenome-assembled genomes (MAGs) belonging to CAP clades IIB (RCAB4-2), IIC (RC14) and II (RC18), from full-scale EBPR sludge for the first time, including a distinct Ca. Accumulibacter clade that is dominant and associated only with the S2EBPR configuration. The results also revealed the temporally increasing predominance of RC14, which belonged to Clade IIC, during the implementation of the S2EBPR configuration. Finally, we also show the existence of previously uncharacterized diversity of clades of CAP, namely the clades IIB and as yet unidentified clade of type II, in full-scale EBPR communities, highlighting the unknown diversity of CAP communities in full-scale EBPR systems.
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Affiliation(s)
- Varun N Srinivasan
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Brown and Caldwell, One Tech Drive, Andover, MA 01810, United States
| | - Guangyu Li
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Dongqi Wang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Nicholas B Tooker
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Department of Civil and Environmental Engineering, University of Massachusetts-Amherst, Amherst, MA 01002, United States
| | - Zihan Dai
- Infrastructure and Environment Division, University of Glasgow, Glasgow G12 8LT, United Kingdom
| | - Annalisa Onnis-Hayden
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Charles Bott
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23454, United States
| | - Paul Dombrowski
- Woodard & Curran, Inc., 1699 King Street, Enfield, CT 06082, United States
| | - Peter Schauer
- Clean Water Services, 16060 SW 85th Avenue, Tigard, OR 97224, United States
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30318, United States
| | - April Z Gu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States; Civil and Environmental Engineering, Cornell University, Ithaca NY 14853, United States.
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14
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McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
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15
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Jha V, Dafale NA, Hathi Z, Purohit H. Genomic and functional potential of the immobilized microbial consortium MCSt-1 for wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:146110. [PMID: 33684742 DOI: 10.1016/j.scitotenv.2021.146110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Treatment of wastewater prior to release in water bodies is an imperative need of the current time to address the global water crises. Thus, consortium MCSt-1 was designed for an effective wastewater treatment based on its cellulolytic, proteolytic, lipolytic, phenol and sodium dodecyl sulfate degrading activities along with effective nutrient removal capacity. Performance of the designed consortium was assayed using two differently configured lab-scale bioreactors as subjected to immobilization on two different matrices (pebbles and nylon mesh). Consortium MCSt-1 proficiently removes soluble chemical oxygen demand, nitrate, ammonia and phosphorus with 83%, 67%, 76%, and 62% removal efficiency, respectively. The immobilization on a mesh is recommended as it exhibited better biofilm formation, hence results in significant organic load and nutrient removal. The functional potential of the consortium MCSt-1 explored through genome characterization and reveal the presence of genes responsible for phosphorus metabolism and removal (pst operon and ppk), ammonia assimilation (amt), and nitrate; nitrite reductase (nar, nir, nor). Additionally, consortium members also annotated with the phenol, catechol and benzoate degradation, stress response, heavy metal and antibiotics resistance genes. Hence, the designed consortium MCSt-1 can withstand the harsh condition of treatment plants and serves as the best solution for enhancing wastewater treatment efficiency.
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Affiliation(s)
- Varsha Jha
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Zubeen Hathi
- City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong Special Administrative Region
| | - Hemant Purohit
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India
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16
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Arumugam K, Bessarab I, Haryono MAS, Liu X, Zuniga-Montanez RE, Roy S, Qiu G, Drautz-Moses DI, Law YY, Wuertz S, Lauro FM, Huson DH, Williams RBH. Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing. NPJ Biofilms Microbiomes 2021; 7:23. [PMID: 33727564 PMCID: PMC7966762 DOI: 10.1038/s41522-021-00196-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023] Open
Abstract
New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
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Affiliation(s)
- Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rogelio E Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue, University of California, Davis, CA, USA
| | - Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Daniel H Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
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17
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Saia SM, Carrick HJ, Buda AR, Regan JM, Walter MT. Critical Review of Polyphosphate and Polyphosphate Accumulating Organisms for Agricultural Water Quality Management. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2722-2742. [PMID: 33559467 DOI: 10.1021/acs.est.0c03566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Despite ongoing management efforts, phosphorus (P) loading from agricultural landscapes continues to impair water quality. Wastewater treatment research has enhanced our knowledge of microbial mechanisms influencing P cycling, especially regarding microbes known as polyphosphate accumulating organisms (PAOs) that store P as polyphosphate (polyP) under oxic conditions and release P under anoxic conditions. However, there is limited application of PAO research to reduce agricultural P loading and improve water quality. Herein, we conducted a meta-analysis to identify articles in Web of Science on polyP and its use by PAOs across five disciplines (i.e., wastewater treatment, terrestrial, freshwater, marine, and agriculture). We also summarized research that provides preliminary support for PAO-mediated P cycling in natural habitats. Terrestrial, freshwater, marine, and agriculture disciplines had fewer polyP and PAO articles compared to wastewater treatment, with agriculture consistently having the least. Most meta-analysis articles did not overlap disciplines. We found preliminary support for PAOs in natural habitats and identified several knowledge gaps and research opportunities. There is an urgent need for interdisciplinary research linking PAOs, polyP, and oxygen availability with existing knowledge of P forms and cycling mechanisms in natural and agricultural environments to improve agricultural P management strategies and achieve water quality goals.
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Affiliation(s)
- Sheila M Saia
- Depatment of Biological and Agricultural Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Hunter J Carrick
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Anthony R Buda
- Pasture Systems and Watershed Management Research Unit, Agricultural Research Service, United States Department of Agriculture, University Park, Pennsylvania 16802, United States
| | - John M Regan
- Department of Civil and Environmental Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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18
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Roy S, Guanglei Q, Zuniga-Montanez R, Williams RB, Wuertz S. Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal. Curr Opin Biotechnol 2021; 67:166-174. [PMID: 33582603 DOI: 10.1016/j.copbio.2021.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/02/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is an efficient, cost-effective, and sustainable method for removing excess phosphorus from wastewater. Polyphosphate accumulating organisms (PAOs) exhibit a unique physiology alternating between anaerobic conditions for uptake of carbon substrates and aerobic or anoxic conditions for phosphorus uptake. The implementation of high-throughput sequencing technologies and advanced molecular tools along with biochemical characterization has provided many new perspectives on the EBPR process. These approaches have helped identify a wide range of carbon substrates and electron acceptors utilized by PAOs that in turn influence interactions with microbial community members and determine overall phosphorus removal efficiency. In this review, we systematically discuss the microbial diversity and metabolic response to a range of environmental conditions and process control strategies in EBPR.
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Affiliation(s)
- Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Qiu Guanglei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Rohan Bh Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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19
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Long S, Yang Y, Pavlostathis SG, Zhao L. Effect of sulfamethoxazole and oxytetracycline on enhanced biological phosphorus removal and bacterial community structure. BIORESOURCE TECHNOLOGY 2021; 319:124067. [PMID: 33035865 DOI: 10.1016/j.biortech.2020.124067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
The individual and combined effects of sulfamethoxazole (SMX) and oxytetracycline (OTC) on an enhanced biological phosphorus removal (EBPR) system was investigated. OTC at 5 mg/L resulted in filamentous bulking with a collapse of EBPR system. P removal decreased to 44.8% and COD was mostly removed during the aerobic phase. SMX and OTC had antagonistic effects in EBPR system. The inhibitory effect of SMX and SMX + OTC on P removal, COD removal, glycogen transformation and extracellular polymeric substances content was reversible with prolonged operation, accompanied with increase of polyphosphate accumulating organisms. The presence of nitrification inhibitor allylthiourea, high pH and low tetX abundance limited the removal of SMX and OTC. The bacterial community structure, antibiotic resistance genes abundances and genes functions were also investigated by metagenomic analysis. The results of this study offer insights into the individual and combined environmental risks of SMX and OTC, and their impact on EBPR.
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Affiliation(s)
- Sha Long
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, USA
| | - Yongkui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Spyros G Pavlostathis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, USA
| | - Lin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
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20
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Roots P, Rosenthal A, Wang Y, Sabba F, Jia Z, Yang F, Zhang H, Kozak J, Wells G. Pushing the limits of solids retention time for enhanced biological phosphorus removal: process characteristics and Accumulibacter population structure. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 82:1614-1627. [PMID: 33107855 DOI: 10.2166/wst.2020.437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Reducing the solids retention time (SRT) of the enhanced biological phosphorus removal (EBPR) process can increase organic carbon diversion to the sidestream for energy recovery, thereby realizing some of the benefits of the high rate activated sludge (HRAS) process. Determining the washout (i.e. minimum) SRT of polyphosphate accumulating organisms (PAOs), therefore, allows for simultaneous phosphorus and carbon diversion for energy recovery from EBPR systems. However, few studies have investigated the washout SRT of PAOs in real wastewater, and little is known of the diversity of PAOs in high rate EBPR systems. Here we demonstrate efficient phosphorus removal (83% orthophosphate removal) in a high rate EBPR sequencing batch reactor fed real primary effluent and operated at 20 °C. Stable operation was achieved at a total SRT of 1.8 ± 0.2 days and hydraulic retention time of 3.7-4.8 hours. 16S rRNA gene sequencing data demonstrated that Accumulibacter were the dominant PAO throughout the study, with a washout aerobic SRT between 0.8 and 1.4 days. qPCR targeting the polyphosphate kinase gene revealed that Accumulibacter clades IIA, IIB and IID dominated the PAO community at low SRT operation, while clade IA was washed out at the lowest SRT values.
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Affiliation(s)
- Paul Roots
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA E-mail:
| | - Alex Rosenthal
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA E-mail:
| | - Yubo Wang
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA E-mail:
| | - Fabrizio Sabba
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA E-mail:
| | - Zhen Jia
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA E-mail:
| | - Fenghua Yang
- Metropolitan Water Reclamation District of Greater Chicago, 6001 W Pershing Road, Chicago, IL, 60804, USA
| | - Heng Zhang
- Metropolitan Water Reclamation District of Greater Chicago, 6001 W Pershing Road, Chicago, IL, 60804, USA
| | - Joseph Kozak
- Metropolitan Water Reclamation District of Greater Chicago, 6001 W Pershing Road, Chicago, IL, 60804, USA
| | - George Wells
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA E-mail:
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21
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Qiu G, Liu X, Saw NMMT, Law Y, Zuniga-Montanez R, Thi SS, Ngoc Nguyen TQ, Nielsen PH, Williams RBH, Wuertz S. Metabolic Traits of Candidatus Accumulibacter clade IIF Strain SCELSE-1 Using Amino Acids As Carbon Sources for Enhanced Biological Phosphorus Removal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2448-2458. [PMID: 31790213 DOI: 10.1021/acs.est.9b02901] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite recent evidence from full-scale plants suggesting that Candidatus Accumulibacter may be capable of using amino acids, this metabolic trait has never been confirmed in a bioreactor experiment. Here we show that an enriched culture of Ca. Accumulibacter clade IIF strain SCELSE-1 could metabolize 11 of 20 α-amino acids, with aspartate, glutamate, asparagine, and glutamine resulting in the highest phosphorus removal. The anaerobic uptake of aspartate and glutamate was achieved through a glutamate/aspartate-proton symporter fully powered by the proton motive force (PMF). Under anaerobic conditions aspartate was deaminized and routed into core carbon metabolic pathways to form polyhydroxyalkanoates (PHA). The lack of genes encoding NADH dependent isocitrate dehydrogenase in the Ca. Accumulibacter genome resulted in a kinetic barrier for glutamate to be channelled to the TCA cycle. Glutamate was stored as glutamate polymer. When amino acids (aspartate or glutamate) and acetate were supplied together, Ca. Accumulibacter took up both carbon sources simultaneously, with the uptake rate of each carbon source largely preserved. Overall energy savings (up to 17%) were achieved under mixed carbon scenarios, due to the ability of Ca. Accumulibacter to rearrange its anaerobic carbon metabolism based on the reducing power, PMF and ATP balance.
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Affiliation(s)
- Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- School of Environment and Energy , South China University of Technology , Guangzhou 510006 , China
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Nay Min Min Thaw Saw
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Yingyu Law
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue , University of California , Davis , California 95616 , United States
| | - Sara Swa Thi
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- Centre for Microbial Communities, Department of Chemistry and Bioscience , Aalborg University , DK-9220 , Aalborg , Denmark
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering , National University of Singapore , Singapore 119077 , Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering , Nanyang Technological University , Singapore 637551 , Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue , University of California , Davis , California 95616 , United States
- School of Civil and Environmental Engineering , Nanyang Technological University , Singapore 639798 , Singapore
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22
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Wang J, Liu X, Jiang X, Zhang L, Hou C, Su G, Wang L, Mu Y, Shen J. Nitrate stimulation of N-Methylpyrrolidone biodegradation by Paracoccus pantotrophus: Metabolite mechanism and Genomic characterization. BIORESOURCE TECHNOLOGY 2019; 294:122185. [PMID: 31569046 DOI: 10.1016/j.biortech.2019.122185] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Due to the toxicological nature of N-methylpyrrolidone (NMP), the conventional anaerobic bioprocess is quite ineffective for NMP removal from wastewater. In order to achieve effective NMP biodegradation under anoxic condition, Paracoccus pantotrophus NJUST38 was isolated for the first time. The supplementation of nitrate into anoxic system resulted in complete removal of 5 mM NMP by NJUST38 within 11 h compared to 24% in the anaerobic control system in the absence of nitrate. Genome characterization revealed that NMP biodegradation catalyzed by several key enzymes/genes, including N-methylhydantoin amidohydrolase (hyuB), methyltransferase (cobA), 4-aminobutyrate-2-oxoglutarate transaminase (gabT), succinate-semialdehyde dehydrogenase (gabD) and so on. NMP biodegradation pathway was proposed based on several intermediates, where NMP was biodegraded mainly for providing electrons and reducing power to support microbial denitrification through tricarboxylic acid (TCA) cycle. The proposed mechanism should aid our mechanistic understanding of NMP biodegradation by Paracoccus pantotrophus and the development of sustainable bioremediation strategies.
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Affiliation(s)
- Jing Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xiaolin Liu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xinbai Jiang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Libin Zhang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Cheng Hou
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Guanyong Su
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Lianjun Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Jinyou Shen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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23
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Profiling population-level diversity and dynamics of Accumulibacter via high throughput sequencing of ppk1. Appl Microbiol Biotechnol 2019; 103:9711-9722. [DOI: 10.1007/s00253-019-10183-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/09/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022]
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24
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Fan YY, Li BB, Yang ZC, Cheng YY, Liu DF, Yu HQ. Mediation of functional gene and bacterial community profiles in the sediments of eutrophic Chaohu Lake by total nitrogen and season. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:233-240. [PMID: 30999200 DOI: 10.1016/j.envpol.2019.04.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/24/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
Microbes in sediments contribute to nutrient release and play an important role in lake eutrophication. However, information about the profiles of functional genes and bacterial communities and the most important environmental factor affecting them in the sediments of eutrophic lake remains unrevealed. In this work, the real-time fluorescent quantitative polymerase chain reaction (qPCR) assay and 16S ribosomal RNA gene next generation sequencing analysis were used to explore the profiles of functional genes and bacterial communities in the sediments of Chaohu Lake. The selected 18 functional genes involved in C, N and P cycles were detected in most of samples. Seasonal variation and sediment variables were found to affect the profiles of functional genes and bacterial communities, and total nitrogen was the dominant environmental factor to drive the formation of bacterial community structure. Proteobacteria and Firmicutes were observed to be the two dominant phyla in the sediments with relative abundance ranging from 10.8% to 36.0% and 7.7%-46.7%, respectively. Three bacterial phyla, i.e., Actinobacteria, Proteobacteria, and Spirochaetes, were found to be significantly positively correlated with the C, N and P-cycle related functional genes. Bacterial community structure was the most important driver to shape the profiles of functional genes. Seasonal variation also influenced the co-occurrence patterns between functional genes and bacterial taxa as revealed by network analysis. The findings from this work facilitate a better understanding about the C, N, and P cycles in the sediments of eutrophic lakes.
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Affiliation(s)
- Yang-Yang Fan
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Bing-Bing Li
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Zong-Chuang Yang
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China
| | - Yuan-Yuan Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China.
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25
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Lv X, Wang D, Iqbal W, Yang B, Mao Y. Microbial reduction of bromate: current status and prospects. Biodegradation 2019; 30:365-374. [PMID: 31236769 DOI: 10.1007/s10532-019-09882-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
Abstract
Bromate is a disinfection byproduct (DBP) that forms during the ozonation of bromide-containing natural water, which may cause health risks to humans. In this review, we provide an overview of the mechanism of bromate formation, microbial communities and bioreactors that are responsible for bromate reduction. Bromate can be formed through two pathways of bromide oxidation by ozone or by ·OH, and it can be removed by biological approaches. Members belonging to phyla of Spirochaetes, Proteobacteria, Firmicutes, Actinobacteria, Clostridium, Deinococcus-Thermus and Bacteroidetes have been identified as capable of reducing bromate to bromide. Multiple configurations of biofilm bioreactors have been employed to cultivate microbial communities to perform bromate removal. The rapid development of multiomics has and will continue to accelerate the elucidation of the mechanisms involved in bromate and other DBP conversions, as well as the interaction patterns among different bacterial subdivisions in the bioremoval of DBPs.
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Affiliation(s)
- Xinyue Lv
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Dan Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Waheed Iqbal
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Bo Yang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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26
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Zhang AN, Mao Y, Wang Y, Zhang T. Mining traits for the enrichment and isolation of not-yet-cultured populations. MICROBIOME 2019; 7:96. [PMID: 31238973 PMCID: PMC6593511 DOI: 10.1186/s40168-019-0708-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. RESULTS Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. CONCLUSION Our method could shed light to the exploration into the bacterial dark matter in the environments.
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Affiliation(s)
- An-Ni Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Yanping Mao
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Yubo Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China.
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27
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Gao H, Mao Y, Zhao X, Liu WT, Zhang T, Wells G. Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess. WATER RESEARCH 2019; 155:275-287. [PMID: 30852315 DOI: 10.1016/j.watres.2019.02.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Denitrification is the stepwise microbial reduction of nitrate or nitrite (NO2-) to nitrogen gas via the obligate intermediates nitric oxide (NO) and nitrous oxide (N2O). Substantial N2O accumulation has been reported in denitrifying enhanced biological phosphorus removal (EBPR) bioreactors enriched in denitrifying polyphosphate accumulating organisms (DPAOs), but little is known about underlying mechanisms for N2O generation, prevalence of complete versus truncated denitrification pathways, or the impact of NO2- feed on DPAO-enriched consortia. To address this knowledge gap, we employed genome-resolved metagenomics to investigate nitrogen transformation potential in a NO2- fed denitrifying EBPR bioreactor enriched in Candidatus Accumulibacter and prone to N2O accumulation. Our analysis yielded 41 near-complete metagenome-assembled genomes (MAGs), including two co-occurring Accumulibacter strains affiliated with clades IA and IC (the first published genome from this clade) and 39 non-PAO flanking bacterial genomes. The dominant Accumulibacter clade IA encoded genes for complete denitrification, while the lower abundance Accumulibacter clade IC harbored all denitrification genes except for a canonical respiratory NO reductase. Analysis of the 39 non-PAO MAGs revealed a high prevalence of taxa harboring an incomplete denitrification pathway. Of the 27 MAGs harboring capacity for at least one step in the denitrification pathway, 10 were putative N2O producers lacking N2O reductase, 16 were putative N2O reducers that lacked at least one upstream denitrification gene, and only one harbored a complete denitrification pathway. We also documented increasing abundance over the course of reactor operation of putative N2O producers. Our results suggest that the unusually high levels of N2O production observed in this Accumulibacter-enriched consortium are linked in part to the selection for non-PAO flanking microorganisms with truncated denitrification pathways.
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Affiliation(s)
- Han Gao
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, United States
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, Shenzhen University, Shenzhen, 518060, PR China; Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong.
| | - Xiaotian Zhao
- Master of Science in Biotechnology Program, McCormick School of Engineering, Northwestern University, Evanston, IL, 60208, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - George Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, United States.
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28
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Zhu J, Liu R, Cao N, Yu J, Liu X, Yu Z. Mycobacterial metabolic characteristics in a water meter biofilm revealed by metagenomics and metatranscriptomics. WATER RESEARCH 2019; 153:315-323. [PMID: 30739073 DOI: 10.1016/j.watres.2019.01.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/27/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Mycobacteria represent one of the most persistent bacterial populations in drinking water distribution system (DWDS) biofilm communities; however, mycobacterial in situ metabolic profiles are largely unknown. In this study, the metabolic characteristics of mycobacteria in a household water meter biofilm were unveiled using a coupled metagenomic/metatranscriptomic approach. The water meter biofilm appeared to express nitrogenase genes (nifDKH) and a full complement of genes coding for several carbon-fixation pathways, especially the Calvin cycle, suggesting the CO2 sequestration and dinitrogen fixation potential of the biofilm. These findings indicate that it may be difficult to prevent the formation of DWDS biofilms simply by controlling the availability of organic carbon or nitrogen. The composite genome of mycobacteria (CG-M) was reconstructed based on the obtained omics data. CG-M shared similar genome phylogeny and virulence-factor profiles with Mycobacterium avium complex, suggesting that population CG-M might represent a member of mycobacteria with pathogenicity. According to the gene expression patterns, population CG-M showed the metabolic potential to assimilate CO2 via the Calvin cycle and/or anaplerotic reactions, and even to grow autotrophically with CO as the sole carbon and energy source. This suggests that organic carbon may not be a limiting factor for mycobacterial growth in DWDSs. Moreover, our results suggest that mycobacterial aromatic degradation is primarily achieved through the catechol meta-cleavage pathway, and biofilm mycobacteria could prefer phosphate as the phosphorus source.
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Affiliation(s)
- Junge Zhu
- University of Chinese Academy of Sciences, Beijing, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruyin Liu
- University of Chinese Academy of Sciences, Beijing, China.
| | - Nan Cao
- Beijing Waterworks Group, Beijing, China
| | - Jianwei Yu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xinchun Liu
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhisheng Yu
- University of Chinese Academy of Sciences, Beijing, China
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29
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Re-evaluating the microbiology of the enhanced biological phosphorus removal process. Curr Opin Biotechnol 2019; 57:111-118. [PMID: 30959426 DOI: 10.1016/j.copbio.2019.03.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/01/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
We have critically assessed some of the dogmas in the microbiology of enhanced biological phosphorus removal (EBPR) and argue that the genus Tetrasphaera can be as important as Ca. Accumulibacter for phosphorus removal; and that proliferation of their competitors, the glycogen accumulating organisms, does not appear to be a practical problem for EBPR efficiency even under tropical conditions. An increasing number of EBPR-related genomes are changing our understanding of their physiology, for example, their potential to participate in denitrification. Rather than trying to identify organisms that adhere to strict phenotype metabolic models, we advocate for broader analyses of the whole microbial communities in EBPR plants by iterative studies with isolates, lab enrichments, and full-scale systems.
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30
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Yu K, Yi S, Li B, Guo F, Peng X, Wang Z, Wu Y, Alvarez-Cohen L, Zhang T. An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community. MICROBIOME 2019; 7:16. [PMID: 30728080 PMCID: PMC6366072 DOI: 10.1186/s40168-019-0634-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/25/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses. RESULTS The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone. CONCLUSION The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.
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Affiliation(s)
- Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China.
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China.
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA.
- Environmental microbiology and bioinformatics Laboratory, Shenzhen Graduate School, Peking University, Nanshan district, Shenzhen, Guangdong, China.
| | - Shan Yi
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA
| | - Bing Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Feng Guo
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Xingxing Peng
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zhiping Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Wu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China.
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31
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Integrated Omic Analyses Provide Evidence that a " Candidatus Accumulibacter phosphatis" Strain Performs Denitrification under Microaerobic Conditions. mSystems 2019; 4:mSystems00193-18. [PMID: 30944872 PMCID: PMC6446978 DOI: 10.1128/msystems.00193-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/13/2018] [Indexed: 11/20/2022] Open
Abstract
The ability of "Candidatus Accumulibacter phosphatis" to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, clarifying the role of "Ca. Accumulibacter phosphatis" in this process has been challenging, since (i) experimental research describes contradictory findings, (ii) none of the published "Ca. Accumulibacter phosphatis" genomes show the existence of a complete respiratory pathway for denitrification, and (iii) some genomes lacking a complete respiratory pathway have genes for assimilatory nitrate reduction. In this study, we used an integrated omics analysis to elucidate the physiology of a "Ca. Accumulibacter phosphatis" strain enriched in a reactor operated under cyclic anaerobic and microaerobic conditions. The reactor's performance suggested the ability of the enriched "Ca. Accumulibacter phosphatis" strain (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under microaerobic conditions. A draft genome of this organism was assembled from metagenomic reads ("Ca. Accumulibacter phosphatis" UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full pathway for respiratory denitrification. The observed transcript abundance patterns showed evidence of coregulation of the denitrifying genes along with a cbb 3 cytochrome, which has been characterized as having high affinity for oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcription-level regulation of both denitrifying and respiratory pathways in UW-LDO-IC. Taking the results together, the omics analysis provides strong evidence that "Ca. Accumulibacter phosphatis" UW-LDO-IC uses oxygen and nitrate simultaneously as electron acceptors under microaerobic conditions. IMPORTANCE "Candidatus Accumulibacter phosphatis" is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that "Ca. Accumulibacter phosphatis" is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.
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Vieira A, Ribera-Guardia A, Marques R, Barreto Crespo MT, Oehmen A, Carvalho G. The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations. Appl Microbiol Biotechnol 2018; 102:6725-6737. [DOI: 10.1007/s00253-018-9077-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 02/06/2018] [Accepted: 05/07/2018] [Indexed: 02/07/2023]
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Zeng W, Zhang L, Fan P, Guo J, Peng Y. Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker. J Environ Sci (China) 2018; 67:237-248. [PMID: 29778158 DOI: 10.1016/j.jes.2017.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/03/2017] [Accepted: 09/04/2017] [Indexed: 06/08/2023]
Abstract
Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A2O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×109 cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A2O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter.
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Affiliation(s)
- Wei Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Limin Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Pengchao Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jingjing Guo
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
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Wang Z, Dunne A, van Loosdrecht MCM, Saikaly PE. Effect of Salt on the Metabolism of ' Candidatus Accumulibacter' Clade I and II. Front Microbiol 2018; 9:479. [PMID: 29616002 PMCID: PMC5865004 DOI: 10.3389/fmicb.2018.00479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/28/2018] [Indexed: 11/29/2022] Open
Abstract
Saline wastewater is known to affect the performance of phosphate-accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) process. However, studies comparing the effect of salinity on different PAO clades are lacking. In this study, ‘Candidatus Accumulibacter phosphatis’ Clade I and II (hereafter referred to as PAOI and PAOII) were highly enriched (∼90% in relative abundance as determined by quantitative FISH) in the form of granules in two sequencing batch reactors. Anaerobic and aerobic batch experiments were conducted to evaluate the effect of salinity on the kinetics and stoichiometry of PAOI and PAOII. PAOI and PAOII communities showed different priority in using polyphosphate (poly-P) and glycogen to generate ATP in the anaerobic phase when exposed to salt, with PAOI depending more on intracellular poly-P degradation (e.g., the proportion of calculated ATP derived from poly-P increased by 5–6% at 0.256 mol/L NaCl or KCl) while PAOII on glycolysis of intracellularly stored glycogen (e.g., the proportion of calculated ATP derived from glycogen increased by 29–30% at 0.256 mol/L NaCl or KCl). In the aerobic phase, the loss of phosphate uptake capability was more pronounced in PAOII due to the higher energy cost to synthesize their larger glycogen pool compared to PAOI. For both PAOI and PAOII, aerobic conversion rates were more sensitive to salt than anaerobic conversion rates. Potassium (K+) and sodium (Na+) ions exhibited different effect regardless of the enriched PAO culture, suggesting that the composition of salt is an important factor to consider when studying the effect of salt on EBPR performance.
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Affiliation(s)
- Zhongwei Wang
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aislinn Dunne
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Pascal E Saikaly
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Liu S, Chen Q, Ma T, Wang M, Ni J. Genomic insights into metabolic potentials of two simultaneous aerobic denitrification and phosphorus removal bacteria, Achromobacter sp. GAD3 and Agrobacterium sp. LAD9. FEMS Microbiol Ecol 2018; 94:4834001. [DOI: 10.1093/femsec/fiy020] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/31/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shufeng Liu
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Tao Ma
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Ming Wang
- Yellow River Institute of Hydraulic Research, Zhengzhou 450003, China
| | - Jinren Ni
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
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Zeng W, Bai X, Guo Y, Li N, Peng Y. Interaction of “ Candidatus Accumulibacter” and nitrifying bacteria to achieve energy-efficient denitrifying phosphorus removal via nitrite pathway from sewage. Enzyme Microb Technol 2017; 105:1-8. [DOI: 10.1016/j.enzmictec.2017.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/29/2022]
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Zhang Y, Yu M, Guo J, Wu D, Hua ZS, Chen GH, Lu H. Spatiotemporal heterogeneity of core functional bacteria and their synergetic and competitive interactions in denitrifying sulfur conversion-assisted enhanced biological phosphorus removal. Sci Rep 2017; 7:10927. [PMID: 28883665 PMCID: PMC5589776 DOI: 10.1038/s41598-017-11448-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/24/2017] [Indexed: 11/09/2022] Open
Abstract
Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) has recently been developed for simultaneously removing nitrogen and phosphorus from saline sewage with minimal sludge production. This novel process could potentially enable sustainable wastewater treatment. Yet, the core functional bacteria and their roles are unknown. Here, we used high-throughput 16S rRNA gene sequencing coupled with principal coordinates analysis and ANOVA with Tukey's test to unravel the spatiotemporal heterogeneity of functional bacteria and their synergetic and competitive interactions. We did not find any obvious spatial heterogeneity within the bacterial population in different size-fractionated sludge samples, but the main functional bacteria varied significantly with operation time. Thauera was enriched (9.26~13.63%) as become the core functional genus in the DS-EBPR reactors and links denitrifying phosphorus removal to sulfide oxidation. The other two functional genera were sulfate-reducing Desulfobacter (4.31~12.85%) and nitrate-reducing and sulfide-oxidizing Thiobacillus (4.79~9.92%). These bacteria cooperated in the DS-EBPR process: Desulfobacter reduced sulfate to sulfide for utilization by Thiobacillus, while Thauera and Thiobacillus competed for nitrate and sulfide as well as Thauera and Desulfobacter competed for acetate. This study is the first to unravel the interactions among core functional bacteria in DS-EBPR, thus improving our understanding of how this removal process works.
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Affiliation(s)
- Yan Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Mei Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Di Wu
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch), Fok Ying Tung Research Institute, The Hong Kong University of Science and Technology, Hong Kong, PR China.
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch), Fok Ying Tung Research Institute, The Hong Kong University of Science and Technology, Hong Kong, PR China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China. .,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China.
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Zeng W, Wang A, Li C, Guo Y, Peng Y. Population dynamics of “ Candidatus Accumulibacter phosphatis” under the modes of complete nitrification and partial nitrification (nitritation) in domestic wastewater treatment system. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Cheng X, Wang J, Chen B, Wang Y, Liu J, Liu L. Effectiveness of phosphate removal during anaerobic digestion of waste activated sludge by dosing iron(III). JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 193:32-39. [PMID: 28188987 DOI: 10.1016/j.jenvman.2017.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/02/2017] [Accepted: 02/05/2017] [Indexed: 06/06/2023]
Abstract
Phosphate-Fe(II) precipitation induced by Fe(III) reduction during the anaerobic digestion of excess activated sludge was investigated for the removal of phosphorus and its possible recovery. The experiments were conducted with three Fe(III) sources at 35 °C and 55 °C. The results show that ferrihydrite-Fe(III) was effectively reduced during the anaerobic sludge digestion by 63% and 96% under mesophilic and thermophilic conditions, respectively. Whereas FeCl3-Fe(III) was only mesophilically reducible and the reduction of hematite-Fe(III) was unnoticeable at either temperature. Efficient precipitation of vivianite was not observed although high saturation index values, e.g., >14 (activity reduction not considered), had been reached. This reveals the complexity of vivianite precipitation in anaerobic digestion systems; for example, Fe(II) complexation and organic interference could not be ignored. With ferrihydrite amendments at a Fe/TP of 1.5, methane production from sludge digestion was reduced by 35.1% at 35 °C, and was unaffected when the digestion temperature went up to 55 °C. But, acidic FeCl3 severely inhibited the methane production and consequently the sludge biomass degradation.
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Affiliation(s)
- Xiang Cheng
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China.
| | - Jue Wang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China
| | - Bing Chen
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China
| | - Yu Wang
- Beijing China Sciences Guoyi Environment Protection Engineering Co., Ltd, No. 8 Caihefang Road, Beijing 100080, China
| | - Jiaqi Liu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China
| | - Lubo Liu
- California State University, Fresno, CA 93740, USA
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Saad SA, Welles L, Abbas B, Lopez-Vazquez CM, van Loosdrecht MCM, Brdjanovic D. Denitrification of nitrate and nitrite by 'Candidatus Accumulibacter phosphatis' clade IC. WATER RESEARCH 2016; 105:97-109. [PMID: 27603967 DOI: 10.1016/j.watres.2016.08.061] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/17/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
Phosphate accumulating organisms (PAO) are assumed to use nitrate as external electron acceptor, allowing an efficient integration of simultaneous nitrogen and phosphate removal with minimal organic carbon (COD) requirements. However, contradicting findings appear in literature regarding the denitrification capacities of PAO due to the lack of clade specific highly enriched PAO cultures. Whereas some studies suggest that only PAO clade I may be capable of using nitrate as external electron acceptor for anoxic P-uptake, other studies indicate that PAO clade II may be responsible for anoxic P-removal. In the present study, a highly enriched PAO clade IC culture (>99% according to FISH) was cultivated in an SBR operated under Anaerobic/Oxic conditions and subsequently exposed to Anaerobic/Anoxic/Oxic conditions using nitrate as electron acceptor. Before and after acclimatization to the presence of nitrate, the aerobic and anoxic (nitrate and nitrite) activities of the PAO I culture were assessed through the execution of batch tests using either acetate or propionate as electron donor. In the presence of nitrate, significant P-uptake by PAO I was not observed before or after acclimatization. Using nitrite as electron acceptor, limited nitrite removal rates were observed before acclimatization with lower rates in the acetate fed reactor without P-uptake and slightly higher in the propionate fed reactor with a marginal anoxic P-uptake. Only after acclimatization to nitrate, simultaneous P and nitrite removal was observed. This study suggests that PAO clade IC is not capable of using nitrate as external electron acceptor for anoxic P-removal. The elucidation of the metabolic capacities for individual PAO clades helps in better understanding and optimization of the relation between microbial ecology and process performance in enhanced biological phosphate removal processes.
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Affiliation(s)
- Sondos A Saad
- Department of Civil Engineering, Faculty of Engineering, Ain Shams University, 1 El Sarayat St., Abbassia, 11517 Cairo, Egypt; Department of Environmental Engineering and Water Technology, UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands.
| | - Laurens Welles
- Department of Environmental Engineering and Water Technology, UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands; Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Carlos M Lopez-Vazquez
- Department of Environmental Engineering and Water Technology, UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Damir Brdjanovic
- Department of Environmental Engineering and Water Technology, UNESCO-IHE Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands; Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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Insights into microbial diversity in wastewater treatment systems: How far have we come? Biotechnol Adv 2016; 34:790-802. [DOI: 10.1016/j.biotechadv.2016.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/15/2016] [Accepted: 04/07/2016] [Indexed: 11/16/2022]
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Mao Y, Wang Z, Li L, Jiang X, Zhang X, Ren H, Zhang T. Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal. PLoS One 2016; 11:e0161506. [PMID: 27547976 PMCID: PMC4993488 DOI: 10.1371/journal.pone.0161506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/05/2016] [Indexed: 01/26/2023] Open
Abstract
A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including Candidatus Competibacter phosphatis and Defluviicoccus-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant Candidatus Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively.
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Affiliation(s)
- Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhiping Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Liguan Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xuxiang Zhang
- School of Environment, Nanjing University, Nanjing, China
| | - Hongqiang Ren
- School of Environment, Nanjing University, Nanjing, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- * E-mail:
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Albertsen M, McIlroy SJ, Stokholm-Bjerregaard M, Karst SM, Nielsen PH. "Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants. Front Microbiol 2016; 7:1033. [PMID: 27458436 PMCID: PMC4930944 DOI: 10.3389/fmicb.2016.01033] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/20/2016] [Indexed: 01/16/2023] Open
Abstract
Enhanced biological phosphorus removal (EBPR) is widely used to remove phosphorus from wastewater. The process relies on polyphosphate accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth, whereby phosphorus can be removed from the wastewater by wasting the biomass. However, glycogen accumulating organisms (GAOs) may reduce the EBPR efficiency as they compete for substrates with PAOs, but do not store excessive amounts of polyphosphate. PAOs and GAOs are thought to be phylogenetically unrelated, with the model PAO being the betaproteobacterial “Candidatus Accumulibacter phosphatis” (Accumulibacter) and the model GAO being the gammaproteobacterial “Candidatus Competibacter phosphatis”. Here, we report the discovery of a GAO from the genus Propionivibrio, which is closely related to Accumulibacter. Propionivibrio sp. are targeted by the canonical fluorescence in situ hybridization probes used to target Accumulibacter (PAOmix), but do not store excessive amounts of polyphosphate in situ. A laboratory scale reactor, operated to enrich for PAOs, surprisingly contained co-dominant populations of Propionivibrio and Accumulibacter. Metagenomic sequencing of multiple time-points enabled recovery of near complete population genomes from both genera. Annotation of the Propionivibrio genome confirmed their potential for the GAO phenotype and a basic metabolic model is proposed for their metabolism in the EBPR environment. Using newly designed fluorescence in situ hybridization (FISH) probes, analyses of full-scale EBPR plants revealed that Propionivibrio is a common member of the community, constituting up to 3% of the biovolume. To avoid overestimation of Accumulibacter abundance in situ, we recommend the use of the FISH probe PAO651 instead of the commonly applied PAOmix probe set.
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Affiliation(s)
- Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Simon J McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Mikkel Stokholm-Bjerregaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark; Krüger A/SAalborg, Denmark
| | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
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Zhang AN, Mao Y, Zhang T. Development of Quantitative Real-time PCR Assays for Different Clades of "Candidatus Accumulibacter". Sci Rep 2016; 6:23993. [PMID: 27142574 PMCID: PMC4855135 DOI: 10.1038/srep23993] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/18/2016] [Indexed: 11/27/2022] Open
Abstract
We designed novel quantitative real-time polymerase chain reaction (qPCR) primers for the polyphosphate kinase 1 (ppk1) gene, targeting eight individual “Candidatus Accumulibacter” (referred to as Accumulibacter) clades. An evaluation of primer sets was conducted regarding the coverage, specificity, and PCR efficiency. (i) All primer sets were designed to cover all available sequences of the target clade. (ii) The phylogenetic analysis of the sequences retrieved from the qPCR products by each primer set demonstrated a high level of specificity. (iii) All calibration curves presented high PCR efficiencies in the range of 85–112% (R2 = 0.962–0.998). In addition, the possible interference of non-target amplicons was individually examined using the qPCR assay for 13 Accumulibacter clades, which were either undetected or showed negligible detection. With the primers designed by other research groups, a highly selective and sensitive qPCR-based method was developed to quantify all Accumulibacter clades, with the exception of Clade IE, in one assay, which enables more comprehensive insights into the community dynamics. The applicability to environmental samples was demonstrated by profiling the Accumulibacter clades in activated sludge samples of nine full-scale wastewater treatment plants.
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Affiliation(s)
- An Ni Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
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Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH. Enhancing metaproteomics--The value of models and defined environmental microbial systems. Proteomics 2016; 16:783-98. [PMID: 26621789 DOI: 10.1002/pmic.201500305] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 12/24/2022]
Abstract
Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.
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Affiliation(s)
- Florian-Alexander Herbst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Vanessa Lünsmann
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Henrik Kjeldal
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin von Bergen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.,Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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46
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Oyserman BO, Noguera DR, del Rio TG, Tringe SG, McMahon KD. Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME JOURNAL 2015; 10:810-22. [PMID: 26555245 PMCID: PMC4796919 DOI: 10.1038/ismej.2015.155] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 01/08/2023]
Abstract
Previous studies on enhanced biological phosphorus removal (EBPR) have focused on reconstructing genomic blueprints for the model polyphosphate-accumulating organism Candidatus Accumulibacter phosphatis. Here, a time series metatranscriptome generated from enrichment cultures of Accumulibacter was used to gain insight into anerobic/aerobic metabolism and regulatory mechanisms within an EBPR cycle. Co-expressed gene clusters were identified displaying ecologically relevant trends consistent with batch cycle phases. Transcripts displaying increased abundance during anerobic acetate contact were functionally enriched in energy production and conversion, including upregulation of both cytoplasmic and membrane-bound hydrogenases demonstrating the importance of transcriptional regulation to manage energy and electron flux during anerobic acetate contact. We hypothesized and demonstrated hydrogen production after anerobic acetate contact, a previously unknown strategy for Accumulibacter to maintain redox balance. Genes involved in anerobic glycine utilization were identified and phosphorus release after anerobic glycine contact demonstrated, suggesting that Accumulibacter routes diverse carbon sources to acetyl-CoA formation via previously unrecognized pathways. A comparative genomics analysis of sequences upstream of co-expressed genes identified two statistically significant putative regulatory motifs. One palindromic motif was identified upstream of genes involved in PHA synthesis and acetate activation and is hypothesized to be a phaR binding site, hence representing a hypothetical PHA modulon. A second motif was identified ~35 base pairs (bp) upstream of a large and diverse array of genes and hence may represent a sigma factor binding site. This analysis provides a basis and framework for further investigations into Accumulibacter metabolism and the reconstruction of regulatory networks in uncultured organisms.
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Affiliation(s)
- Ben O Oyserman
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, USA
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, USA
| | | | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, USA
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47
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Ju F, Zhang T. Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12628-40. [PMID: 26451629 DOI: 10.1021/acs.est.5b03719] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.
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Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong , Hong Kong SRA, China
| | - Tong Zhang
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong , Hong Kong SRA, China
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48
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Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL. Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm. Environ Microbiol 2015; 18:273-87. [PMID: 26279094 DOI: 10.1111/1462-2920.13019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 11/30/2022]
Abstract
Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal. Reactors formed two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods, we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high-stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.
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Affiliation(s)
- Jeremy J Barr
- Department of Biology, San Diego State University, San Diego, CA, USA.,Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomedical Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Connor T Skennerton
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Toshikazu Fukushima
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Division of Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Marcus L Hastie
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Jeffrey J Gorman
- Protein Discovery Centre, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Gene W Tyson
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Philip L Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.,Environmental Biotechnology Cooperative Research Centre (EBCRC), Sydney, NSW, Australia
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49
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Wong DHJ, Beiko RG. Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. BMC Genomics 2015; 16:526. [PMID: 26173980 PMCID: PMC4502571 DOI: 10.1186/s12864-015-1752-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/06/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways. RESULTS The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture. CONCLUSIONS Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.
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Affiliation(s)
- Dennis H-J Wong
- Faculty of Graduate Studies, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
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50
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Mao Y, Graham DW, Tamaki H, Zhang T. Dominant and novel clades of Candidatus Accumulibacter phosphatis in 18 globally distributed full-scale wastewater treatment plants. Sci Rep 2015; 5:11857. [PMID: 26138542 PMCID: PMC4490554 DOI: 10.1038/srep11857] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/09/2015] [Indexed: 11/09/2022] Open
Abstract
Here we employed quantitative real-time PCR (qPCR) assays for polyphosphate kinase 1 (ppk1) and 16S rRNA genes to assess relative abundances of dominant clades of Candidatus Accumulibacter phosphatis (referred to Accumulibacter) in 18 globally distributed full-scale wastewater treatment plants (WWTPs) from six countries. Accumulibacter were not only detected in the 6 WWTPs performing biological phosphorus removal, but also inhabited in the other 11 WWTPs employing conventional activated sludge (AS) with abundances ranging from 0.02% to 7.0%. Among the AS samples, clades IIC and IID were found to be dominant among the five Accumulibacter clades. The relative abundance of each clade in the Accumulibacter lineage significantly correlated (p < 0.05) with the influent total phosphorus and chemical oxygen demand instead of geographical factors (e.g. latitude), which showed that the local wastewater characteristics and WWTPs configurations could be more significant to determine the proliferation of Accumulibacter clades in full-scale WWTPs rather than the geographical location. Moreover, two novel Accumulibacter clades (IIH and II-I) which had not been previously detected were discovered in two enhanced biological phosphorus removal (EBPR) WWTPs. The results deepened our understanding of the Accumulibacter diversity in environmental samples.
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Affiliation(s)
- Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - David W Graham
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
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